Understanding the conservation and function of regulatory elements using data-driven approaches

Cardiff University Cardiff School of Biosciences

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Dr Nathan Harmston No more applications being accepted Funded PhD Project (UK Students Only)

Cardiff United Kingdom Bioinformatics Cancer Biology Data Science Developmental Biology Machine Learning

Cardiff School of Biosciences, Cardiff University

About the Project

The precise regulation of gene expression is necessary for development, with its dysregulation leading to disease. In multicellular organisms, gene expression is regulated by elements called promoters and enhancers. The DNA sequences of these elements contains the information necessary for determining which transcription factors bind and what their downstream effect on expression is. However, mapping between the sequence of an enhancer or promoter, known as its regulatory grammar, and its function is nontrivial. This project has the overall aim of providing a better understanding the regulatory grammar of enhancers and promoters with a focus on two key questions/features: · conservation - some regulatory elements are highly conserved over large evolutionary distances, whereas other enhancers only exhibit conservation over smaller distances. Are there features of enhancers that distinguish between these different patterns? · cell-type specificity - activation of the same signalling pathway in two distinct cell types can regulate two completely distinct sets of genes. How is this information encoded in the sequence of enhancers? This project is completely computational and includes data analysis and machine learning components, and will include the analysis of high-throughput sequencing datasets (ChIP-seq, RNA-seq).

Application deadline: 31st March 2024 with interviews (either in person or by Skype) being held on or around 8th April 2024.

How to apply:

You can apply online - consideration is automatic on applying for a PhD in Biosciences, with an October 2024 start date.

Please use our online application service at https://www.cardiff.ac.uk/study/postgraduate/research/programmes/programme/biosciences-phd-mphil-md

and specify in the funding section state that you wish to be considered for School of Biosciences funding.

Please specify that you are applying for this particular project and the supervisor.

Information on the application process can be found here

http://www.cardiff.ac.uk/study/pos tgraduate/applying

Funding Notes

The School of Biosciences is funding this studentship and the award offered will cover Home fees and maintenance stipend.

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